Table 2 Comparison of memory between the JA algorithm and our algorithm on an input with 8 million reads from a plant genome.
From: Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
JA ALGO | ParBiConstruct | ||||||
|---|---|---|---|---|---|---|---|
P | k | RES.MEM(Mb) | SHR.MEM(Mb) | RES.MEM(Mb) | efficiency | SHR.MEM(Mb) | efficiency |
8 | 21 | 903.714 | 3.690 | 244.603 | 3.695 | 3.328 | 1.109 |
8 | 27 | 675.516 | 3.638 | 146.750 | 4.603 | 3.232 | 1.126 |
8 | 33 | 289.787 | 3.588 | 62.580 | 4.631 | 3.007 | 1.193 |
8 | 35 | 116.938 | 7.527 | 14.625 | 7.996 | 2.397 | 3.140 |
12 | 21 | 681.664 | 4.782 | 156.875 | 4.345 | 4.256 | 1.124 |
12 | 27 | 265.304 | 6.882 | 91.219 | 2.908 | 3.889 | 1.769 |
12 | 33 | 241.630 | 4.721 | 46.805 | 5.163 | 3.675 | 1.285 |
12 | 35 | 94.548 | 7.518 | 12.276 | 7.702 | 2.771 | 2.713 |
16 | 21 | 501.175 | 5.726 | 152.995 | 3.276 | 5.175 | 1.107 |
16 | 27 | 333.487 | 11.730 | 77.523 | 4.302 | 4.823 | 2.432 |
16 | 33 | 166.395 | 5.714 | 42.746 | 3.893 | 4.628 | 1.235 |
16 | 35 | 68.851 | 8.172 | 13.578 | 5.071 | 3.443 | 2.374 |
24 | 21 | 344.888 | 8.081 | 105.723 | 3.262 | 7.133 | 1.133 |
24 | 27 | 214.681 | 16.271 | 61.674 | 3.481 | 6.690 | 2.432 |
24 | 33 | 115.630 | 7.830 | 34.583 | 3.344 | 5.959 | 1.314 |
24 | 35 | 52.110 | 10.082 | 15.990 | 3.259 | 4.472 | 2.254 |
32 | 21 | 260.063 | 10.413 | 86.157 | 3.018 | 9.070 | 1.148 |
32 | 27 | 179.657 | 20.550 | 49.737 | 3.612 | 8.096 | 2.538 |
32 | 33 | 95.790 | 9.968 | 34.180 | 2.803 | 7.495 | 1.330 |
32 | 35 | 47.602 | 11.290 | 15.289 | 3.113 | 4.905 | 2.302 |
48 | 21 | 186.225 | 14.109 | 71.073 | 2.620 | 12.405 | 1.137 |
48 | 27 | 112.237 | 19.623 | 47.596 | 2.358 | 11.255 | 1.744 |
48 | 33 | 75.059 | 11.996 | 30.929 | 2.427 | 9.070 | 1.323 |
48 | 35 | 37.500 | 10.643 | 19.576 | 1.916 | 6.764 | 1.573 |
64 | 21 | 150.324 | 17.311 | 63.449 | 2.369 | 14.640 | 1.182 |
64 | 27 | 105.692 | 23.570 | 43.590 | 2.425 | 12.975 | 1.817 |
64 | 33 | 66.095 | 14.168 | 31.853 | 2.075 | 10.653 | 1.330 |
64 | 35 | 38.823 | 12.159 | 22.275 | 1.743 | 8.096 | 1.502 |